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Leon, Claire, and Sherry prepare to leave the police station and go to the sewer system, but along the way they encounter the creature with the bulbous eyeball on its shoulder. Wielding a pipe, it attacks them and proves to be a formidable opponent. It begins to attack wildly, and eventually tires before falling over the railing and into the abyss. The bridge collapses from the strain of the fighting, and Leon falls down after him into the sewer. Upon recovering, he finds Ada again. She's trapped in a gun fight with another woman, who calls her a "thief". Ada plans to make a maneuver, and Leon can see she'll leave herself wide open. As Ada moves and the woman takes aim, Leon jumps between them and takes a bullet to the back. The woman runs off, and Ada tends to Leon's wounds. He inquires about the altercation, and senses Ada won't be as forthcoming as he wants her to be. He insists she tell him more, but she reluctantly declines as she views the contents of a familiar looking pendant.

While Sherry was lost in the sewer system, she encountered her father. William was able to implant his embyros into her, and she is now infected. Leon and Claire leave the sewer, proceed through the factory and find themselves in the Underground Lab. They drop off Sherry in the Security Office and decide to find a way to cure her G-Virus infection. When they leave, Annette contacts Leon through his radio. She warns him about Ada, stating she is not to be trusted. As they go through the lab, Trenchy rears his ugly head again, and this time they run away from him as Ada watches from the shadows. Throughout the lab, they find that the area has been overcome by a montrous plant, smaller but still dangerous plants called Ivy walk around, and that the Lickers have become much more powerful. They eventually travel down a corridor and overhear Annette confronting Birkin, who has mutated into a second, more grotesque form. She attempts to reason with him, but upon sensing her ill intentions he attacks her. Leon and Claire find her bleeding out. She tells them how to create the G-Vaccine and tells them to inform Sherry that she loved her. They proceed down to the P-4 Lab and process the antidote, but they're soon confronted by Trenchy again. They lure him to the power room's blast furnace near an iron smelting pit. There they make their last stand. His attacks end up damaging a control panel, which causes a malfunction in the system that threats to activate a self-destruct mechanism inside the facility. After luring him to the lowest level, they engage him. Trenchy appears to have the upper hand until Ada arrives. After knocking him down, Ada prepares to shoot him in the head, but the monster recovers quickly. In a panic Ada pulls the trigger, temporarily blinding him. He savagely throws Ada against a wall and falls into the smelting pool. Ada however, is critically wounded by the Tyrant and as Leon approaches she tells him to leave. Leon refuses, but Ada reassures him that he must escape alone. She kisses him and "dies".